Isidore Rigoutsos | bioRxiv Science

bioRxiv2016

Comments on: "A comprehensive repertoire of tRNA-derived fragments in prostate cancer"

We evaluated the deep-sequencing (RNA-seq) data from human prostate tissue that were reported in [1] and the tRNA-derived fragments described in the original analysis. Our study of the same RNA-seq datasets reveals a considerably different pool of tRNA fragments, many of them with higher abundances than the fragments reported in [1]. We also evaluated the q-PCR approach proposed in [1]. As the approach lacks 5-endpoint specificity, it will not estimate correctly the abundance of many of the tRFs that are present in the sampled RNA populations from human prostate tissue.

Cancer Biology↗

bioRxiv2014

N-BLR, a primate-specific non-coding transcript, modulates the epithelial-to-mesenchymal transition and leads to colorectal cancer invasion and migration

Non-coding RNAs have been commanding increasingly greater attention in recent years as the few that have been functionalized to date play important roles in key cellular processes. Here we show that N-BLR, a ~900 bp non-coding RNA, modulates the epithelial-to-mesenchymal transition, increases colorectal cancer invasion, and functions as a migration enabler by affecting the expression of ZEB1 and E-cadherin. In patients with colorectal cancer, N-BLR expression associates with tumor stage and invasion potential. As N-BLR contains several instances of a category of DNA motifs known as pyknons, we also designed a custom-made array to investigate the possibility that other pyknon loci may be transcribed. For several of the loci probed by the array we found that the corresponding pyknons are differentially expressed between cancer and normal tissue samples. Taken together the data suggest that a systematic study of other pyknon-containing non-coding RNAs like N-BLR may be warranted in the context of colorectal cancer.

Genomics↗